<div dir="ltr">Thanks to Dr. Pavel and Dr. Fischmann for useful discussion and views on Omit map,<div>and how to remove a possible bias.</div><div><br></div><div>Regards</div><div>Manoj</div><div><br><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 16, 2015 at 9:53 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Hi,<span class=""><br>
<br>
<blockquote type="cite">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">What
Pavel describes is how to get a “difference map”. But it is
not an “omit map” per the original definition.</span></p>
</div>
</blockquote>
<br></span>
perhaps we are getting into terminology here.. I'm sticking to the
original paper by T. Bhat.<br>
<br>
Difference map is F1-F2, F1=w1*Fobs, F2=w2*Fmodel. I believe you can
prefix it with "omit" if you omit something (remove part of model)
from F2.<span class=""><br>
<br>
<blockquote type="cite">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u>The
omitted part should never have been part of the model during
any refinement step before the omit map is calculated. The
purpose is to prevent bias.</span></p>
</div>
</blockquote>
<br></span>
This is where it gets into nuances not discussed in the original
paper, if memory serves.<span class=""><br>
<br>
<blockquote type="cite">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u>If
the model has already been refined with a ligand, then the
technique of simulated annealing refinement can be used to
remove the bias after removing the ligand. This approximates
an “omit map” (still one may argue not a real “omit map”,
but close enough).</span><br>
</p>
</div>
</blockquote>
<br></span>
Yes, this seems to be the common mindset. But I'm yet to see a
convincing example with clear illustration of such bias. I believe
this<br>
<br>
1) remove ligand;<br>
2) do some refinement (optionally, don't believe really necessary!);<br>
3) compute mFo-DFc map;<br>
<br>
should be good enough in most cases.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
<br>
</font></span></div>
</blockquote></div><br></div>